Multiple sequence alignment - TraesCS1B01G437100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G437100 chr1B 100.000 2857 0 0 1 2857 659987751 659990607 0.000000e+00 5276
1 TraesCS1B01G437100 chr1B 87.626 695 55 16 1191 1865 659997510 659998193 0.000000e+00 778
2 TraesCS1B01G437100 chr1D 85.685 1949 164 48 873 2792 474753157 474755019 0.000000e+00 1947
3 TraesCS1B01G437100 chr1D 91.667 876 47 14 1 869 474752040 474752896 0.000000e+00 1190
4 TraesCS1B01G437100 chr1A 85.244 1945 183 50 873 2792 570264988 570266853 0.000000e+00 1906
5 TraesCS1B01G437100 chr3D 82.635 835 125 15 1938 2766 515188675 515187855 0.000000e+00 721
6 TraesCS1B01G437100 chr7A 74.538 703 151 22 1987 2679 20640241 20640925 6.030000e-72 281
7 TraesCS1B01G437100 chr5A 85.000 240 27 3 1966 2205 536851962 536852192 4.760000e-58 235
8 TraesCS1B01G437100 chr5B 80.556 180 30 3 2490 2668 9806369 9806194 1.790000e-27 134
9 TraesCS1B01G437100 chr6B 73.375 323 71 10 2007 2319 667201004 667200687 3.890000e-19 106


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G437100 chr1B 659987751 659990607 2856 False 5276.0 5276 100.000 1 2857 1 chr1B.!!$F1 2856
1 TraesCS1B01G437100 chr1B 659997510 659998193 683 False 778.0 778 87.626 1191 1865 1 chr1B.!!$F2 674
2 TraesCS1B01G437100 chr1D 474752040 474755019 2979 False 1568.5 1947 88.676 1 2792 2 chr1D.!!$F1 2791
3 TraesCS1B01G437100 chr1A 570264988 570266853 1865 False 1906.0 1906 85.244 873 2792 1 chr1A.!!$F1 1919
4 TraesCS1B01G437100 chr3D 515187855 515188675 820 True 721.0 721 82.635 1938 2766 1 chr3D.!!$R1 828
5 TraesCS1B01G437100 chr7A 20640241 20640925 684 False 281.0 281 74.538 1987 2679 1 chr7A.!!$F1 692

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
679 685 0.111253 AGGCCAACCTCTTCCACAAG 59.889 55.0 5.01 0.0 46.34 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 2971 0.179073 GGCTTTGCAGGCTCGATCTA 60.179 55.0 12.3 0.0 42.53 1.98 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 26 2.861974 GGAGTTGGGGTGGGGGAA 60.862 66.667 0.00 0.00 0.00 3.97
91 94 4.112634 TGCCCCTCTTGTATTGACTTTT 57.887 40.909 0.00 0.00 0.00 2.27
122 125 5.590530 AGATGAGTACTCAGTGGTGAATC 57.409 43.478 28.29 18.43 43.61 2.52
124 127 5.359576 AGATGAGTACTCAGTGGTGAATCTC 59.640 44.000 28.29 17.15 43.61 2.75
125 128 4.667573 TGAGTACTCAGTGGTGAATCTCT 58.332 43.478 21.74 0.00 34.14 3.10
131 137 9.256228 AGTACTCAGTGGTGAATCTCTTATTTA 57.744 33.333 0.00 0.00 30.14 1.40
132 138 9.871238 GTACTCAGTGGTGAATCTCTTATTTAA 57.129 33.333 0.00 0.00 30.14 1.52
152 158 8.926715 ATTTAAGTGTTTCTCTTGTGTTTTCC 57.073 30.769 0.00 0.00 0.00 3.13
153 159 4.616181 AGTGTTTCTCTTGTGTTTTCCG 57.384 40.909 0.00 0.00 0.00 4.30
154 160 3.105937 GTGTTTCTCTTGTGTTTTCCGC 58.894 45.455 0.00 0.00 0.00 5.54
155 161 2.750166 TGTTTCTCTTGTGTTTTCCGCA 59.250 40.909 0.00 0.00 0.00 5.69
196 202 2.644299 TGTTCATCCTCACATCCACCTT 59.356 45.455 0.00 0.00 0.00 3.50
205 211 4.503910 CTCACATCCACCTTCAATTCGTA 58.496 43.478 0.00 0.00 0.00 3.43
225 231 2.125106 GATCGGGCCACCTCACAC 60.125 66.667 4.39 0.00 33.28 3.82
226 232 4.082523 ATCGGGCCACCTCACACG 62.083 66.667 4.39 0.00 33.28 4.49
235 241 1.271163 CCACCTCACACGGTTTACCAT 60.271 52.381 0.00 0.00 34.29 3.55
238 244 2.073816 CCTCACACGGTTTACCATGTC 58.926 52.381 0.00 0.00 40.93 3.06
249 255 4.048504 GTTTACCATGTCTTGCAACAACC 58.951 43.478 0.00 0.00 31.81 3.77
255 261 1.039856 GTCTTGCAACAACCACCCAT 58.960 50.000 0.00 0.00 0.00 4.00
271 277 4.955450 CCACCCATCCTCAAACAAATATCA 59.045 41.667 0.00 0.00 0.00 2.15
283 289 8.408043 TCAAACAAATATCATTTGTCCTCACT 57.592 30.769 15.50 0.00 41.30 3.41
342 348 1.742768 CCTCTAGCCAACCCTAGCG 59.257 63.158 0.00 0.00 35.78 4.26
344 350 1.676678 CTCTAGCCAACCCTAGCGCA 61.677 60.000 11.47 0.00 35.78 6.09
355 361 1.269569 CCCTAGCGCATTATCACACGA 60.270 52.381 11.47 0.00 0.00 4.35
359 365 2.279741 AGCGCATTATCACACGACATT 58.720 42.857 11.47 0.00 0.00 2.71
393 399 9.106070 TCATTTCTCTCACATATCAGACAATTG 57.894 33.333 3.24 3.24 0.00 2.32
394 400 8.890718 CATTTCTCTCACATATCAGACAATTGT 58.109 33.333 11.78 11.78 0.00 2.71
395 401 7.838771 TTCTCTCACATATCAGACAATTGTG 57.161 36.000 17.58 2.37 39.16 3.33
396 402 6.343703 TCTCTCACATATCAGACAATTGTGG 58.656 40.000 17.58 8.17 38.52 4.17
397 403 4.877823 TCTCACATATCAGACAATTGTGGC 59.122 41.667 17.58 2.05 38.52 5.01
399 405 5.988287 TCACATATCAGACAATTGTGGCTA 58.012 37.500 17.58 4.45 43.33 3.93
400 406 6.051074 TCACATATCAGACAATTGTGGCTAG 58.949 40.000 17.58 2.40 43.33 3.42
401 407 4.818546 ACATATCAGACAATTGTGGCTAGC 59.181 41.667 17.58 6.04 43.33 3.42
405 411 3.515502 TCAGACAATTGTGGCTAGCTAGT 59.484 43.478 17.58 1.73 43.33 2.57
424 430 7.433680 AGCTAGTTAACCTCCAAAATTGTTTG 58.566 34.615 0.88 0.00 43.26 2.93
436 442 1.174712 ATTGTTTGACTGCGGCTGCT 61.175 50.000 20.27 0.00 43.34 4.24
437 443 0.533978 TTGTTTGACTGCGGCTGCTA 60.534 50.000 20.27 4.21 43.34 3.49
471 477 6.577103 TGGATGTTGTTTTATTTCTGTTGCA 58.423 32.000 0.00 0.00 0.00 4.08
486 492 0.612732 TTGCAGGATTTCAGCCCAGG 60.613 55.000 0.00 0.00 0.00 4.45
545 551 0.182537 TTCTCCACCCACAACACCAG 59.817 55.000 0.00 0.00 0.00 4.00
547 553 0.819259 CTCCACCCACAACACCAGTG 60.819 60.000 0.00 0.00 36.76 3.66
578 584 1.667830 ATGCGTGAAGACCACACCG 60.668 57.895 0.00 0.00 45.98 4.94
580 586 2.308039 GCGTGAAGACCACACCGAC 61.308 63.158 0.00 0.00 45.98 4.79
615 621 6.002653 ACCTAACTTGGTTCTCAAAAGTCT 57.997 37.500 0.00 0.00 36.89 3.24
624 630 6.565234 TGGTTCTCAAAAGTCTCGATATCTC 58.435 40.000 0.34 0.00 0.00 2.75
679 685 0.111253 AGGCCAACCTCTTCCACAAG 59.889 55.000 5.01 0.00 46.34 3.16
686 692 2.338809 ACCTCTTCCACAAGACCATCA 58.661 47.619 0.00 0.00 34.71 3.07
738 746 3.790437 CAGACTGGCCGCCCTCAT 61.790 66.667 7.03 0.00 0.00 2.90
739 747 2.041922 AGACTGGCCGCCCTCATA 60.042 61.111 7.03 0.00 0.00 2.15
740 748 1.689233 AGACTGGCCGCCCTCATAA 60.689 57.895 7.03 0.00 0.00 1.90
744 752 0.466189 CTGGCCGCCCTCATAATGTT 60.466 55.000 7.03 0.00 0.00 2.71
746 754 0.385390 GGCCGCCCTCATAATGTTTG 59.615 55.000 0.00 0.00 0.00 2.93
798 806 1.344763 CTCGAGTTGGTTTGGGACTCT 59.655 52.381 3.62 0.00 38.08 3.24
799 807 1.070134 TCGAGTTGGTTTGGGACTCTG 59.930 52.381 0.00 0.00 38.08 3.35
801 809 0.535102 AGTTGGTTTGGGACTCTGCG 60.535 55.000 0.00 0.00 0.00 5.18
827 835 1.260561 CCTTTGGTCTCGACAACAACG 59.739 52.381 0.00 0.00 0.00 4.10
869 877 1.758862 CCATCCTTTGGGAGATTTGGC 59.241 52.381 0.00 0.00 45.86 4.52
870 878 1.758862 CATCCTTTGGGAGATTTGGCC 59.241 52.381 0.00 0.00 45.86 5.36
871 879 0.783206 TCCTTTGGGAGATTTGGCCA 59.217 50.000 0.00 0.00 36.57 5.36
886 1151 7.099120 AGATTTGGCCATGATTGTTTAAAGAC 58.901 34.615 6.09 0.00 0.00 3.01
988 1254 4.309950 GTGCCCACGGACGGTTCT 62.310 66.667 0.00 0.00 0.00 3.01
1033 1299 0.317938 GCTCGTACTAGGACATGGCG 60.318 60.000 5.80 0.00 0.00 5.69
1055 1336 0.034089 ACGTAGTAGTTAGGGCGGGT 60.034 55.000 0.00 0.00 41.94 5.28
1086 1367 4.597004 AGAGAACCGGATGTTACAGTAGA 58.403 43.478 9.46 0.00 37.29 2.59
1248 1529 3.827898 CGGGCTCTGGAGACGGAC 61.828 72.222 5.24 0.00 42.04 4.79
1366 1653 2.202946 TGTCGGCAAAGACGTGCA 60.203 55.556 0.00 0.00 46.81 4.57
1380 1667 1.701545 CGTGCAACTGTTCGTGGTGT 61.702 55.000 0.00 0.00 31.75 4.16
1386 1673 2.838693 TGTTCGTGGTGTCCCGGA 60.839 61.111 0.73 0.00 0.00 5.14
1420 1710 3.822192 CGACAGCGTCATCCCCGA 61.822 66.667 8.91 0.00 32.09 5.14
1545 1835 3.330720 AGCCCTTCCAACTCCGGG 61.331 66.667 0.00 0.00 39.76 5.73
1546 1836 3.327404 GCCCTTCCAACTCCGGGA 61.327 66.667 0.00 0.00 39.08 5.14
1771 2084 4.672587 TTGGTCTGCATACATCCTACTC 57.327 45.455 4.48 0.00 0.00 2.59
1820 2133 7.003939 TGCTTGTTGTACTATTTCATCATCG 57.996 36.000 0.00 0.00 0.00 3.84
1865 2178 7.643764 CGGAGCGTGTAAAATCAATTTCATATT 59.356 33.333 0.00 0.00 32.27 1.28
1895 2216 5.425217 GGGGGTGAATTTCATATGTTCCTTT 59.575 40.000 1.78 0.00 0.00 3.11
1922 2243 6.959361 ACTTTATGCAGTACACTTTGTTCAG 58.041 36.000 0.00 0.00 0.00 3.02
1925 2246 8.439993 TTTATGCAGTACACTTTGTTCAGTAA 57.560 30.769 0.00 0.00 0.00 2.24
1933 2254 8.582437 AGTACACTTTGTTCAGTAATGCTACTA 58.418 33.333 0.00 0.00 36.14 1.82
1934 2255 7.653767 ACACTTTGTTCAGTAATGCTACTAC 57.346 36.000 0.00 0.00 36.14 2.73
1935 2256 7.442656 ACACTTTGTTCAGTAATGCTACTACT 58.557 34.615 0.00 0.00 36.14 2.57
1936 2257 7.931948 ACACTTTGTTCAGTAATGCTACTACTT 59.068 33.333 0.00 0.00 36.14 2.24
1937 2258 9.419297 CACTTTGTTCAGTAATGCTACTACTTA 57.581 33.333 0.00 0.00 36.14 2.24
1938 2259 9.991906 ACTTTGTTCAGTAATGCTACTACTTAA 57.008 29.630 0.00 0.00 36.14 1.85
1960 2281 1.364901 GCTTACGCCCCGCTGTATA 59.635 57.895 0.00 0.00 0.00 1.47
1962 2283 1.607251 GCTTACGCCCCGCTGTATAAT 60.607 52.381 0.00 0.00 0.00 1.28
1972 2293 4.328983 CCCCGCTGTATAATTATAGCAACG 59.671 45.833 16.70 16.26 41.28 4.10
1973 2294 4.328983 CCCGCTGTATAATTATAGCAACGG 59.671 45.833 24.50 24.50 41.28 4.44
2016 2341 5.050837 GCAAACAACACATCAAGCCTAAAAG 60.051 40.000 0.00 0.00 0.00 2.27
2017 2342 6.272318 CAAACAACACATCAAGCCTAAAAGA 58.728 36.000 0.00 0.00 0.00 2.52
2018 2343 6.463995 AACAACACATCAAGCCTAAAAGAA 57.536 33.333 0.00 0.00 0.00 2.52
2019 2344 6.463995 ACAACACATCAAGCCTAAAAGAAA 57.536 33.333 0.00 0.00 0.00 2.52
2020 2345 6.872920 ACAACACATCAAGCCTAAAAGAAAA 58.127 32.000 0.00 0.00 0.00 2.29
2021 2346 7.327214 ACAACACATCAAGCCTAAAAGAAAAA 58.673 30.769 0.00 0.00 0.00 1.94
2022 2347 7.492344 ACAACACATCAAGCCTAAAAGAAAAAG 59.508 33.333 0.00 0.00 0.00 2.27
2023 2348 7.346751 ACACATCAAGCCTAAAAGAAAAAGA 57.653 32.000 0.00 0.00 0.00 2.52
2024 2349 7.781056 ACACATCAAGCCTAAAAGAAAAAGAA 58.219 30.769 0.00 0.00 0.00 2.52
2025 2350 7.922811 ACACATCAAGCCTAAAAGAAAAAGAAG 59.077 33.333 0.00 0.00 0.00 2.85
2026 2351 8.137437 CACATCAAGCCTAAAAGAAAAAGAAGA 58.863 33.333 0.00 0.00 0.00 2.87
2027 2352 8.695456 ACATCAAGCCTAAAAGAAAAAGAAGAA 58.305 29.630 0.00 0.00 0.00 2.52
2054 2383 4.336993 AGAAAGTAATGTCAACAACGGCAA 59.663 37.500 0.00 0.00 0.00 4.52
2067 2396 0.599204 ACGGCAACTCGATGAAACGT 60.599 50.000 0.00 0.00 34.70 3.99
2129 2460 1.770061 ACACTCCAAGTACCCCGAAAA 59.230 47.619 0.00 0.00 0.00 2.29
2133 2464 0.250989 CCAAGTACCCCGAAAAGCCA 60.251 55.000 0.00 0.00 0.00 4.75
2149 2480 1.164041 GCCACGTACCAAGCAACACT 61.164 55.000 0.00 0.00 0.00 3.55
2198 2529 1.302033 GCTGCCCGGATATGTCCTG 60.302 63.158 0.73 0.00 42.73 3.86
2207 2538 2.172717 CGGATATGTCCTGGGGTTTTCT 59.827 50.000 6.95 0.00 42.73 2.52
2245 2576 1.349542 TGGGGAATGGGTACATCCGG 61.350 60.000 0.00 0.00 35.94 5.14
2282 2615 2.753043 GGCACCCACAGGCATCAG 60.753 66.667 0.00 0.00 36.11 2.90
2308 2641 0.682209 GGTGCCAGATGAGCCAACAT 60.682 55.000 0.00 0.00 0.00 2.71
2362 2696 2.088104 TGATCCGTAGCCTTCCATCT 57.912 50.000 0.00 0.00 0.00 2.90
2377 2711 0.254178 CATCTAGCTTGCCACCCACT 59.746 55.000 0.00 0.00 0.00 4.00
2394 2728 1.592400 CTAGCATGCGCCATCACGA 60.592 57.895 13.01 0.00 39.83 4.35
2396 2730 0.945743 TAGCATGCGCCATCACGATC 60.946 55.000 13.01 0.00 39.83 3.69
2399 2733 0.877213 CATGCGCCATCACGATCTGA 60.877 55.000 4.18 0.00 34.06 3.27
2474 2808 0.911769 ATGGGAGTGCAAGGAATCGA 59.088 50.000 0.00 0.00 0.00 3.59
2483 2817 0.179073 CAAGGAATCGAGGACGGCAT 60.179 55.000 0.00 0.00 40.21 4.40
2521 2855 1.304381 GGAAATGCCTCCACTGCCA 60.304 57.895 0.00 0.00 35.36 4.92
2527 2861 4.147449 CCTCCACTGCCATCGCGA 62.147 66.667 13.09 13.09 38.08 5.87
2567 2901 4.451150 CTTCGCAGTAGCCGGCCA 62.451 66.667 26.15 6.66 37.52 5.36
2570 2904 4.227134 CGCAGTAGCCGGCCAGAT 62.227 66.667 26.15 7.06 37.52 2.90
2574 2908 4.530857 GTAGCCGGCCAGATGCGT 62.531 66.667 26.15 3.86 42.61 5.24
2620 2978 1.528542 CCAGACGGGCCTAGATCGA 60.529 63.158 0.84 0.00 0.00 3.59
2624 2982 2.598985 CGGGCCTAGATCGAGCCT 60.599 66.667 19.03 4.19 46.31 4.58
2694 3053 1.141881 CCCAGAATCCCGACTCACG 59.858 63.158 0.00 0.00 42.18 4.35
2704 3063 2.265904 CGACTCACGACCTCCACCA 61.266 63.158 0.00 0.00 45.77 4.17
2706 3065 2.156051 GACTCACGACCTCCACCACC 62.156 65.000 0.00 0.00 0.00 4.61
2710 3069 2.603473 CGACCTCCACCACCAGGA 60.603 66.667 0.00 0.00 38.69 3.86
2765 3127 2.360191 GGCTCAGATGGGCCCAAA 59.640 61.111 32.58 13.99 42.30 3.28
2782 3144 2.447047 CCAAAGGGGCCATATCTAGGTT 59.553 50.000 4.39 0.00 0.00 3.50
2785 3147 3.074857 AGGGGCCATATCTAGGTTGAA 57.925 47.619 4.39 0.00 0.00 2.69
2792 3154 3.134081 CCATATCTAGGTTGAACGGGTGT 59.866 47.826 0.00 0.00 0.00 4.16
2793 3155 4.369182 CATATCTAGGTTGAACGGGTGTC 58.631 47.826 0.00 0.00 0.00 3.67
2794 3156 1.707106 TCTAGGTTGAACGGGTGTCA 58.293 50.000 0.00 0.00 0.00 3.58
2795 3157 2.253610 TCTAGGTTGAACGGGTGTCAT 58.746 47.619 0.00 0.00 0.00 3.06
2796 3158 3.433343 TCTAGGTTGAACGGGTGTCATA 58.567 45.455 0.00 0.00 0.00 2.15
2797 3159 2.762535 AGGTTGAACGGGTGTCATAG 57.237 50.000 0.00 0.00 0.00 2.23
2798 3160 1.278127 AGGTTGAACGGGTGTCATAGG 59.722 52.381 0.00 0.00 0.00 2.57
2799 3161 1.084289 GTTGAACGGGTGTCATAGGC 58.916 55.000 0.00 0.00 0.00 3.93
2800 3162 0.981183 TTGAACGGGTGTCATAGGCT 59.019 50.000 0.00 0.00 0.00 4.58
2801 3163 0.249120 TGAACGGGTGTCATAGGCTG 59.751 55.000 0.00 0.00 0.00 4.85
2802 3164 1.078426 AACGGGTGTCATAGGCTGC 60.078 57.895 0.00 0.00 0.00 5.25
2803 3165 1.836999 AACGGGTGTCATAGGCTGCA 61.837 55.000 0.50 0.00 0.00 4.41
2804 3166 1.815421 CGGGTGTCATAGGCTGCAC 60.815 63.158 0.50 0.99 33.68 4.57
2805 3167 1.452108 GGGTGTCATAGGCTGCACC 60.452 63.158 17.92 17.92 44.55 5.01
2817 3179 4.314440 TGCACCTCCGCAGACCAC 62.314 66.667 0.00 0.00 36.86 4.16
2819 3181 4.394712 CACCTCCGCAGACCACCC 62.395 72.222 0.00 0.00 0.00 4.61
2820 3182 4.640690 ACCTCCGCAGACCACCCT 62.641 66.667 0.00 0.00 0.00 4.34
2821 3183 3.775654 CCTCCGCAGACCACCCTC 61.776 72.222 0.00 0.00 0.00 4.30
2822 3184 4.135153 CTCCGCAGACCACCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
2826 3188 4.767255 GCAGACCACCCTCGCCAG 62.767 72.222 0.00 0.00 0.00 4.85
2827 3189 4.767255 CAGACCACCCTCGCCAGC 62.767 72.222 0.00 0.00 0.00 4.85
2832 3194 4.641645 CACCCTCGCCAGCACCAA 62.642 66.667 0.00 0.00 0.00 3.67
2833 3195 4.335647 ACCCTCGCCAGCACCAAG 62.336 66.667 0.00 0.00 0.00 3.61
2834 3196 4.335647 CCCTCGCCAGCACCAAGT 62.336 66.667 0.00 0.00 0.00 3.16
2835 3197 2.743928 CCTCGCCAGCACCAAGTC 60.744 66.667 0.00 0.00 0.00 3.01
2836 3198 2.031012 CTCGCCAGCACCAAGTCA 59.969 61.111 0.00 0.00 0.00 3.41
2837 3199 2.280797 TCGCCAGCACCAAGTCAC 60.281 61.111 0.00 0.00 0.00 3.67
2838 3200 3.357079 CGCCAGCACCAAGTCACC 61.357 66.667 0.00 0.00 0.00 4.02
2839 3201 2.985847 GCCAGCACCAAGTCACCC 60.986 66.667 0.00 0.00 0.00 4.61
2840 3202 2.282462 CCAGCACCAAGTCACCCC 60.282 66.667 0.00 0.00 0.00 4.95
2841 3203 2.669569 CAGCACCAAGTCACCCCG 60.670 66.667 0.00 0.00 0.00 5.73
2842 3204 4.643387 AGCACCAAGTCACCCCGC 62.643 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 25 3.364460 AAAAAGGCAAGCAAAGGGTTT 57.636 38.095 0.00 0.00 30.99 3.27
67 70 3.118531 AGTCAATACAAGAGGGGCATCT 58.881 45.455 0.00 0.00 0.00 2.90
91 94 7.396339 ACCACTGAGTACTCATCTTATAACACA 59.604 37.037 25.35 0.00 39.13 3.72
111 114 8.553459 ACACTTAAATAAGAGATTCACCACTG 57.447 34.615 7.17 0.00 37.08 3.66
113 116 9.827411 GAAACACTTAAATAAGAGATTCACCAC 57.173 33.333 7.17 0.00 36.47 4.16
131 137 4.674362 GCGGAAAACACAAGAGAAACACTT 60.674 41.667 0.00 0.00 0.00 3.16
132 138 3.181500 GCGGAAAACACAAGAGAAACACT 60.181 43.478 0.00 0.00 0.00 3.55
154 160 3.510388 TGAAGAGCACGAGGAACTATG 57.490 47.619 0.00 0.00 41.55 2.23
155 161 3.449018 ACATGAAGAGCACGAGGAACTAT 59.551 43.478 0.00 0.00 41.55 2.12
196 202 2.093394 TGGCCCGATCTTTACGAATTGA 60.093 45.455 0.00 0.00 0.00 2.57
205 211 1.299976 GTGAGGTGGCCCGATCTTT 59.700 57.895 0.00 0.00 35.12 2.52
225 231 2.292016 TGTTGCAAGACATGGTAAACCG 59.708 45.455 0.00 0.00 39.43 4.44
226 232 4.048504 GTTGTTGCAAGACATGGTAAACC 58.951 43.478 0.00 0.00 0.00 3.27
235 241 0.323816 TGGGTGGTTGTTGCAAGACA 60.324 50.000 0.00 0.00 0.00 3.41
238 244 0.318120 GGATGGGTGGTTGTTGCAAG 59.682 55.000 0.00 0.00 0.00 4.01
249 255 6.720112 ATGATATTTGTTTGAGGATGGGTG 57.280 37.500 0.00 0.00 0.00 4.61
255 261 7.669304 TGAGGACAAATGATATTTGTTTGAGGA 59.331 33.333 17.85 2.64 42.11 3.71
271 277 4.307032 ACCATTGCTAGTGAGGACAAAT 57.693 40.909 0.00 0.00 0.00 2.32
283 289 1.717032 AGGCGGATCTACCATTGCTA 58.283 50.000 7.22 0.00 38.90 3.49
342 348 4.568359 AGAGTCAATGTCGTGTGATAATGC 59.432 41.667 0.00 0.00 0.00 3.56
344 350 7.716612 TGATAGAGTCAATGTCGTGTGATAAT 58.283 34.615 0.00 0.00 32.78 1.28
355 361 7.845037 TGTGAGAGAAATGATAGAGTCAATGT 58.155 34.615 0.00 0.00 40.97 2.71
359 365 9.359653 TGATATGTGAGAGAAATGATAGAGTCA 57.640 33.333 0.00 0.00 42.06 3.41
393 399 2.764572 TGGAGGTTAACTAGCTAGCCAC 59.235 50.000 20.91 13.76 33.94 5.01
394 400 3.110293 TGGAGGTTAACTAGCTAGCCA 57.890 47.619 20.91 14.36 33.94 4.75
395 401 4.482952 TTTGGAGGTTAACTAGCTAGCC 57.517 45.455 20.91 13.27 33.94 3.93
396 402 6.374613 ACAATTTTGGAGGTTAACTAGCTAGC 59.625 38.462 20.91 6.62 33.94 3.42
397 403 7.923414 ACAATTTTGGAGGTTAACTAGCTAG 57.077 36.000 19.44 19.44 33.94 3.42
398 404 8.573035 CAAACAATTTTGGAGGTTAACTAGCTA 58.427 33.333 5.42 0.00 38.82 3.32
399 405 7.286775 TCAAACAATTTTGGAGGTTAACTAGCT 59.713 33.333 5.42 0.00 42.23 3.32
400 406 7.381408 GTCAAACAATTTTGGAGGTTAACTAGC 59.619 37.037 5.42 0.00 42.23 3.42
401 407 8.630037 AGTCAAACAATTTTGGAGGTTAACTAG 58.370 33.333 5.42 0.00 42.23 2.57
405 411 6.045955 GCAGTCAAACAATTTTGGAGGTTAA 58.954 36.000 0.00 0.00 42.23 2.01
424 430 2.447244 ATATCTTAGCAGCCGCAGTC 57.553 50.000 0.00 0.00 42.27 3.51
471 477 1.005215 CTTGACCTGGGCTGAAATCCT 59.995 52.381 0.00 0.00 0.00 3.24
486 492 3.545633 GAAGCGTTGTCATTGTCTTGAC 58.454 45.455 0.00 0.00 45.05 3.18
528 534 0.819259 CACTGGTGTTGTGGGTGGAG 60.819 60.000 0.00 0.00 0.00 3.86
551 557 2.350522 GTCTTCACGCATGAGGATGTT 58.649 47.619 0.00 0.00 42.39 2.71
578 584 0.600782 TTAGGTTCGGCGTTGTGGTC 60.601 55.000 6.85 0.00 0.00 4.02
580 586 0.601841 AGTTAGGTTCGGCGTTGTGG 60.602 55.000 6.85 0.00 0.00 4.17
615 621 1.880675 GAAGCCAGTCGGAGATATCGA 59.119 52.381 0.00 0.00 40.67 3.59
624 630 1.668419 CCCAAATAGAAGCCAGTCGG 58.332 55.000 0.00 0.00 0.00 4.79
679 685 4.194640 ACATGCTATTGTGAGTGATGGTC 58.805 43.478 0.00 0.00 0.00 4.02
707 713 1.194781 AGTCTGCCGTGTTCCCATCT 61.195 55.000 0.00 0.00 0.00 2.90
732 740 3.217626 GAGAGCCCAAACATTATGAGGG 58.782 50.000 14.37 14.37 42.55 4.30
733 741 3.629398 GTGAGAGCCCAAACATTATGAGG 59.371 47.826 0.00 0.00 0.00 3.86
734 742 3.629398 GGTGAGAGCCCAAACATTATGAG 59.371 47.826 0.00 0.00 0.00 2.90
735 743 3.010027 TGGTGAGAGCCCAAACATTATGA 59.990 43.478 0.00 0.00 0.00 2.15
736 744 3.355378 TGGTGAGAGCCCAAACATTATG 58.645 45.455 0.00 0.00 0.00 1.90
737 745 3.624777 CTGGTGAGAGCCCAAACATTAT 58.375 45.455 0.00 0.00 0.00 1.28
738 746 2.879756 GCTGGTGAGAGCCCAAACATTA 60.880 50.000 0.00 0.00 32.35 1.90
739 747 1.915141 CTGGTGAGAGCCCAAACATT 58.085 50.000 0.00 0.00 0.00 2.71
740 748 0.610232 GCTGGTGAGAGCCCAAACAT 60.610 55.000 0.00 0.00 32.35 2.71
827 835 0.034089 AGAGCTACCCATGGCCAAAC 60.034 55.000 10.96 0.00 31.21 2.93
861 869 7.099120 GTCTTTAAACAATCATGGCCAAATCT 58.901 34.615 10.96 0.00 0.00 2.40
863 871 6.650390 GTGTCTTTAAACAATCATGGCCAAAT 59.350 34.615 10.96 3.31 0.00 2.32
886 1151 4.143115 ACAACGAACGCTGAAATAGATGTG 60.143 41.667 4.67 0.00 0.00 3.21
941 1206 2.046217 GAACCCGCCTTCCACTCC 60.046 66.667 0.00 0.00 0.00 3.85
988 1254 2.824936 CTCAGCTTCTCCTCTCAACTCA 59.175 50.000 0.00 0.00 0.00 3.41
1033 1299 1.604278 CCGCCCTAACTACTACGTACC 59.396 57.143 0.00 0.00 0.00 3.34
1055 1336 1.176619 TCCGGTTCTCTTCTCACGCA 61.177 55.000 0.00 0.00 0.00 5.24
1086 1367 2.614983 GCTCTCGCTACAGCTACTAGTT 59.385 50.000 0.00 0.00 39.32 2.24
1349 1636 1.815840 TTGCACGTCTTTGCCGACA 60.816 52.632 0.00 0.00 42.25 4.35
1351 1638 1.522806 AGTTGCACGTCTTTGCCGA 60.523 52.632 0.00 0.00 42.25 5.54
1366 1653 1.227438 CGGGACACCACGAACAGTT 60.227 57.895 0.00 0.00 36.13 3.16
1545 1835 4.660938 ACCCCCTTGCGCTTGGTC 62.661 66.667 9.73 0.00 0.00 4.02
1546 1836 4.660938 GACCCCCTTGCGCTTGGT 62.661 66.667 9.73 7.80 0.00 3.67
1590 1898 0.522180 CGTAAGAGCTCCAGACGTGT 59.478 55.000 19.23 0.00 43.02 4.49
1761 2074 7.304497 AGTACAAACTCAAAGAGTAGGATGT 57.696 36.000 0.00 6.58 42.59 3.06
1786 2099 2.298411 ACAACAAGCAAACAAGCAGG 57.702 45.000 0.00 0.00 36.85 4.85
1820 2133 4.263435 TCCGGTCACCAATAATACAAACC 58.737 43.478 0.00 0.00 0.00 3.27
1872 2193 6.154363 TCAAAGGAACATATGAAATTCACCCC 59.846 38.462 10.38 0.00 0.00 4.95
1895 2216 6.935741 ACAAAGTGTACTGCATAAAGTTCA 57.064 33.333 0.00 0.00 0.00 3.18
1922 2243 8.538039 CGTAAGCCTTTTAAGTAGTAGCATTAC 58.462 37.037 0.00 0.00 0.00 1.89
1950 2271 4.328983 CCGTTGCTATAATTATACAGCGGG 59.671 45.833 29.63 20.60 46.98 6.13
1956 2277 4.925054 TCCGTGCCGTTGCTATAATTATAC 59.075 41.667 0.81 0.73 38.71 1.47
1960 2281 2.319136 TCCGTGCCGTTGCTATAATT 57.681 45.000 0.00 0.00 38.71 1.40
1962 2283 2.319136 ATTCCGTGCCGTTGCTATAA 57.681 45.000 0.00 0.00 38.71 0.98
1972 2293 1.819632 CCAGCAGGTATTCCGTGCC 60.820 63.158 8.48 0.00 38.05 5.01
1973 2294 1.819632 CCCAGCAGGTATTCCGTGC 60.820 63.158 0.00 5.16 37.79 5.34
2021 2346 9.396022 TGTTGACATTACTTTCTCTTTTCTTCT 57.604 29.630 0.00 0.00 0.00 2.85
2023 2348 9.788960 GTTGTTGACATTACTTTCTCTTTTCTT 57.211 29.630 0.00 0.00 0.00 2.52
2024 2349 8.122952 CGTTGTTGACATTACTTTCTCTTTTCT 58.877 33.333 0.00 0.00 0.00 2.52
2025 2350 7.376072 CCGTTGTTGACATTACTTTCTCTTTTC 59.624 37.037 0.00 0.00 0.00 2.29
2026 2351 7.193595 CCGTTGTTGACATTACTTTCTCTTTT 58.806 34.615 0.00 0.00 0.00 2.27
2027 2352 6.725246 CCGTTGTTGACATTACTTTCTCTTT 58.275 36.000 0.00 0.00 0.00 2.52
2036 2365 3.551551 GAGTTGCCGTTGTTGACATTAC 58.448 45.455 0.00 0.00 0.00 1.89
2054 2383 2.607187 GTCATCCACGTTTCATCGAGT 58.393 47.619 0.00 0.00 34.70 4.18
2129 2460 1.147376 TGTTGCTTGGTACGTGGCT 59.853 52.632 0.00 0.00 0.00 4.75
2133 2464 2.634600 TGAAAGTGTTGCTTGGTACGT 58.365 42.857 0.00 0.00 37.52 3.57
2149 2480 3.303725 CGTTGTCGCATTCCTTCTTGAAA 60.304 43.478 0.00 0.00 0.00 2.69
2198 2529 3.053896 CGTGCCGGAGAAAACCCC 61.054 66.667 5.05 0.00 0.00 4.95
2308 2641 5.432645 GTTTTTGGGTTTTGGAGAAATCCA 58.567 37.500 0.00 0.00 33.93 3.41
2319 2652 3.108376 TGGCTAGTGGTTTTTGGGTTTT 58.892 40.909 0.00 0.00 0.00 2.43
2362 2696 1.198094 TGCTAGTGGGTGGCAAGCTA 61.198 55.000 7.97 0.00 40.22 3.32
2377 2711 0.945743 GATCGTGATGGCGCATGCTA 60.946 55.000 17.13 2.12 42.25 3.49
2394 2728 2.047274 CGTGGGTGGCGTTCAGAT 60.047 61.111 0.00 0.00 0.00 2.90
2396 2730 3.041940 GACGTGGGTGGCGTTCAG 61.042 66.667 0.00 0.00 43.04 3.02
2399 2733 4.955774 GACGACGTGGGTGGCGTT 62.956 66.667 4.58 0.00 43.04 4.84
2474 2808 3.133014 CCTCGATGATGCCGTCCT 58.867 61.111 0.00 0.00 0.00 3.85
2494 2828 4.796495 GGCATTTCCCTCCCGCGT 62.796 66.667 4.92 0.00 0.00 6.01
2521 2855 2.043852 AGTGACCTCCCTCGCGAT 60.044 61.111 10.36 0.00 0.00 4.58
2551 2885 4.451150 CTGGCCGGCTACTGCGAA 62.451 66.667 28.56 1.03 40.82 4.70
2556 2890 4.227134 CGCATCTGGCCGGCTACT 62.227 66.667 28.56 5.19 40.31 2.57
2567 2901 4.479993 GCCCCTGCTGACGCATCT 62.480 66.667 0.00 0.00 46.74 2.90
2574 2908 3.957586 CTGGTGTGCCCCTGCTGA 61.958 66.667 0.00 0.00 38.71 4.26
2613 2971 0.179073 GGCTTTGCAGGCTCGATCTA 60.179 55.000 12.30 0.00 42.53 1.98
2694 3053 3.393360 CTCCTGGTGGTGGAGGTC 58.607 66.667 2.09 0.00 45.39 3.85
2704 3063 1.330655 CGATGGTGTAGCCTCCTGGT 61.331 60.000 0.00 0.00 38.35 4.00
2706 3065 0.103208 GTCGATGGTGTAGCCTCCTG 59.897 60.000 0.00 0.00 38.35 3.86
2710 3069 1.478510 CTTCTGTCGATGGTGTAGCCT 59.521 52.381 0.00 0.00 38.35 4.58
2762 3124 3.138283 TCAACCTAGATATGGCCCCTTTG 59.862 47.826 0.00 0.00 0.00 2.77
2765 3127 2.711547 GTTCAACCTAGATATGGCCCCT 59.288 50.000 0.00 0.00 0.00 4.79
2769 3131 2.104281 ACCCGTTCAACCTAGATATGGC 59.896 50.000 0.00 0.00 0.00 4.40
2778 3140 1.278127 CCTATGACACCCGTTCAACCT 59.722 52.381 0.00 0.00 0.00 3.50
2782 3144 0.249120 CAGCCTATGACACCCGTTCA 59.751 55.000 0.00 0.00 0.00 3.18
2785 3147 2.290287 TGCAGCCTATGACACCCGT 61.290 57.895 0.00 0.00 0.00 5.28
2800 3162 4.314440 GTGGTCTGCGGAGGTGCA 62.314 66.667 3.37 0.00 43.95 4.57
2802 3164 4.394712 GGGTGGTCTGCGGAGGTG 62.395 72.222 3.37 0.00 0.00 4.00
2803 3165 4.640690 AGGGTGGTCTGCGGAGGT 62.641 66.667 3.37 0.00 0.00 3.85
2804 3166 3.775654 GAGGGTGGTCTGCGGAGG 61.776 72.222 3.37 0.00 0.00 4.30
2805 3167 4.135153 CGAGGGTGGTCTGCGGAG 62.135 72.222 0.00 0.00 0.00 4.63
2809 3171 4.767255 CTGGCGAGGGTGGTCTGC 62.767 72.222 0.00 0.00 0.00 4.26
2810 3172 4.767255 GCTGGCGAGGGTGGTCTG 62.767 72.222 0.00 0.00 0.00 3.51
2815 3177 4.641645 TTGGTGCTGGCGAGGGTG 62.642 66.667 0.00 0.00 0.00 4.61
2816 3178 4.335647 CTTGGTGCTGGCGAGGGT 62.336 66.667 0.00 0.00 0.00 4.34
2817 3179 4.335647 ACTTGGTGCTGGCGAGGG 62.336 66.667 0.00 0.00 0.00 4.30
2818 3180 2.743928 GACTTGGTGCTGGCGAGG 60.744 66.667 0.00 0.00 0.00 4.63
2819 3181 2.031012 TGACTTGGTGCTGGCGAG 59.969 61.111 0.00 0.00 0.00 5.03
2820 3182 2.280797 GTGACTTGGTGCTGGCGA 60.281 61.111 0.00 0.00 0.00 5.54
2821 3183 3.357079 GGTGACTTGGTGCTGGCG 61.357 66.667 0.00 0.00 0.00 5.69
2822 3184 2.985847 GGGTGACTTGGTGCTGGC 60.986 66.667 0.00 0.00 0.00 4.85
2823 3185 2.282462 GGGGTGACTTGGTGCTGG 60.282 66.667 0.00 0.00 0.00 4.85
2824 3186 2.669569 CGGGGTGACTTGGTGCTG 60.670 66.667 0.00 0.00 0.00 4.41
2825 3187 4.643387 GCGGGGTGACTTGGTGCT 62.643 66.667 0.00 0.00 0.00 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.